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Top Forums Shell Programming and Scripting awk to match file1 and extract specific tag values Post 303028307 by MadeInGermany on Friday 4th of January 2019 04:42:44 AM
Old 01-04-2019
I think you want a lookup table from file1: $1 is the lookup key and $2 the returned value.
Code:
# in file 1 store the $2 values in s[$1] (s[] indexed by $1)
FNR==NR {
  s[$1]=$2
  next
}

Now you can test existence with (key in s) or get the value with s[key] or loop through the keys with for (key in s).

I think the following captures the wanted values in file2:
Code:
{
  match($8,/'normalizedPos':'([^']+)'/, pos)  # extract value after : into pos[]
  match((";" $8),/;(AF=[^;]+).*;(FDP=[^;]+)/, info) # extract values after AF= and FDP= into info[]
  match($8,/'gene':'([^']+)'/,gene) # extract the value after gene into gene[]
  print "pos[1]="pos[1], "info[1]="info[1], "info[2]="info[2], "gene[1]="gene[1]
}

Note1: the target array as 3rd argument is an extension in GNU-awk. (Maybe you want to consider perl? Then it works on all platforms that have perl.)
Note2: for a most exact string match use a "border character". I have even prepended a ";" to the input string for match() in order to ensure it exists even at the beginning.
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h5diff(1)						      General Commands Manual							 h5diff(1)

NAME
h5diff - Compares two HDF5 files and reports the differences. SYNOPSIS
h5diff file1 file2 [OPTIONS] [object1 [object2 ] ] DESCRIPTION
h5diff is a command line tool that compares two HDF5 files, file1 and file2, and reports the differences between them. Optionally, h5diff will compare two objects within these files. If only one object, object1, is specified, h5diff will compare object1 in file1 with object1 in file2. In two objects, object1 and object2, are specified, h5diff will compare object1 in file1 with object2 in file2. These objects must be HDF5 datasets. object1 and object2 must be expressed as absolute paths from the respective file's root group. Additional information, with several sample cases, can be found in the document H5diff Examples. OPTIONS
file1 file2 The HDF5 files to be compared. -h Print all differences. -r Print only the names of objects that differ; do not print the differences. These objects may be HDF5 datasets, groups, or named datatypes. -n count Print difference up to count differences, then stop. count must be a positive integer. -d delta Print only differences that are greater than the limit delta. delta must be a positive number. The comparison criterion is whether the absolute value of the difference of two corresponding values is greater than delta (e.g., |a-b| > delta, where a is a value in file1 and b is a value in file2). -p relative Print only differences that are greater than a relative error. relative must be a positive number. The comparison criterion is whether the absolute value of the difference 1 and the ratio of two corresponding values is greater than relative (e.g., |1-(b/a)| > relative where a is a value in file1 and b is a value in file2). object1 object2 Specific object(s) within the files to be compared. EXAMPLES
The following h5diff call compares the object /a/b in file1 with the object /a/c in file2: h5diff file1 file2 /a/b /a/c This h5diff call compares the object /a/b in file1 with the same object in file2: h5diff file1 file2 /a/b And this h5diff call compares all objects in both files: h5diff file1 file2 SEE ALSO
h5dump(1), h5ls(1), h5repart(1), h5import(1), gif2h5(1), h52gif(1), h5perf(1) h5diff(1)
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